BIOCHEMISTRY REVIEWER
table present before: Hydrogen,
TOPIC: Introduction to Biomolecules
Biochemistry
 Study of life and its chemical Reactions
 Bio (Life) Chemistry (Chemical Reactions)
 The chemistry of living organisms
 Combines aspects of all the field of
chemistry
What is Biochem?
 See all the living or once living things
around you? The process that allows them
to grow, multiply, age is all biochemical in
nature.
Biochemist
 Person who study’s biochemistry or the
chemical reaction that occur at the
molecular level of organisms.
!!BIOCHEMISTRY is similar to molecular biology:
Both fields study living systems at the molecular
level, but biochemist concentrate on the chemical
reactions that occur.!!
Biochemical Substance
 Chemical substances found within a living
organism.
 Divided into 2 groups: BIOINORGANIC
SUBSTANCES AND BIOOGANIC SUBSTANCES
 BIOINORGANIC SUBSTANCES includes water
and organic salt. Do not contain carbon.
 BIOORGANIC SUBSTANCES includes
carbohydrate, lipids, proteins, and nucleic
acid. Contains carbon.
TOPIC: Beginnings of BIOLOGY: Origin of
Life
Bigbang Theory (Cataclysmic Explosion)
 Widely accepted cosmological
theory for the origin of the universe.
 According to bigbang cosmology, all
the matter in the universe was
originally confined to a o Passive Transport - doesn’t
comparatively small amount of
space.
 3 Smallest chemical in the periodic
Lithium, Helion. The only 3 elements
of the earth before.
The Rest of the Chemical Elements are thought to
have been formed in 3 ways:
1. By thermonuclear reactions that
normally take place in star.
2. In explosion of Star.
3. By action of the cosmic rays outside
the stars since the formation of the
galaxy.
Types of living Cells
 Cells some in 2 types: Prokaryotes
and Eukaryotes (Viruses also bear
similarities to the cells, but these are
limited. Many scientific don’t
consider Viruses “Living”)
1. Prokaryotes
 Mostly Bacteria, and no nucleus
 Has few defined structures
 Has 3 components: a cell wall, and
membrane, and plasma membrane.
This wall allows a controlled passage
of materials into and out the cells.
2. Eukaryotes
 Are animals, plants, fungi
 Has nucleus
 Eukaryotes cells have number of
membranes closed components
known as Organelles,
The Primary Components of Animals Cells
Includes:
 Plasma Membrane
 Separates material inside the cell
from everything outside the cells.
 Transport thru its membrane may be
active or passive:
o Active Transport – Requires
ticket (Energy or ATP) to
enter or to leave the cell.
require a ticket. Includes
diffusion, osmosis, filtration.
  Centrioles  Contain protein and Ribonucleic
 Cell train conductors acids subunits.
 Organized structural components of  Amino acids are assembled into
the cell like microtubules, which proteins.
help move the cell parts during cell *Enzymes- Parts of nearly every process
division. that occurs in the organisms
 Small Vacuoles
Parts of the CELLS:  Also known as simply vacuoles
 Storage and Transport of materials
 Endoplasmic Reticulum  Stored materials may be for later use
 Main part of cell factory or maybe waste materials that cells
 Shipping department no longer needs.
 2 types: ROUGH AND SMOOTH ER
o Rough Endoplasmic Brief Work at Plant Cells:
Reticulum – Contains  Plant Cells
Ribosomes  Cell contains same components as
o Smooth Endoplasmic animal cells, plus a cell wall, a large
Reticulum – Does not contain vacuole, and in the case of green
Ribosomes. plants chloroplasts.
 Golgi Apparatus
 Serves as cell’s postal system. Parts of Plant Ceils:
 Looks like a maze.  Cell Wall
 Responsible for cell packaging the  Is composed of cellulose (Like starch,
vesicles (small membranes – is polymer glucose).
enclosed sacs)  Provide structure and rigidity.
 Lysosomes  Large Vacuole
 Landfills  Serves as warehouse for the large
 Contain digestive enzymes that starch molecule.
break down substances that harm o Glucose – Which is produce by
the cells. photosynthesis, is converted to
 Mitochondria starch (a polymer of glucose). At
 Cells power plant (powerhouse), some time, this starch is available as
where cells produce energy. an energy source.
 (Singular Mitochondrion)  Chloroplasts
 Use food, primarily the  Present in green plants
carbohydrates, glucose, to produce  Specialized chemical factories, site of
energy, which comes from breaking photosynthesis
down (ATP: Adenosine  Chlorophyll gives color to the plants
Triphosphate). (green).
 Nucleus/Nucleolus  Ribosomes
 Cell’s control center – Host the DNA  Particle that is present in large
all future generations originated number in all cells and serves as the
(DNA – Genes) site of protein synthesis.
 Nucleus contains chromatin.  Endoplasmic Reticulum
 During cell division, the chromatin  Important Particularly, in the
separates into chromosomes. synthesis, folding, modification, and
 Ribosomes transport of protein.
 Nucleolus
  Site of ribosomes biogenesis, which  Process is converted chemical
synthesis of ribosomes. energy, resulting in the production
 Participates and play a role in cells of oxygen and energy-rich organic
response to stress. compound.
 Nucleoli – Made of proteins, DNA and RNA  Green algae that site of
 Small bodies seen within nucleus. photosynthesis
 Gel-Like matrix  Mitochondrion
 Nucleus  Membrane-bound organelles found
 Control and regulates the activities in the cytoplasm of almost all
of the cell. eukaryotic cells.
 Carries gene.  Generates large quantities of energy
 Nuclear Membrane in the form ATP.
 Also called nuclear envelope NOTE:
 Double membrane layer that  Photosynthesis – conversion of light energy
separates the contents of the from sun light into minerals to the plants.
nucleus from the rest of the cell  Starch - Energy Source
 Barrier protects cell DNA from  Chromosomes – DNA itself
chemical reactions.
 Leucoplast TOPIC: Chemical Bonding
 Stores starch, lipids, and protein.
 Only found in plant cells Chemical Bonding
 Used to distinguish between a plant  Provides the energy necessary to
and animal cell. hold two different atoms together as
 Cell Membrane part of a chemical compound.
 (Also known as plasma  Strength of the bond depends on
membrane/Cytoplasmic Membrane) the molecules or atoms involved in
 (Historically referred to as the the process of bond formation.
plasmalemma) MATTER
 Separates and protects the inferior  Atoms
of the cell from outside.  Smallest unit of matter
 Golgi Complex  Composed of electron, protons, and
 Responsible for transporting, neutrons
modifying, and packaging proteins  Basic Building Blocks
and lipids into vesicles for delivery.  Examples: Oxygen, Hydrogen,
 Vacuoles Nitrogen
 Essential Cytoplasmic orans  Elements
(Organelles).  Pure substances consisting of one
 Responsible for storage, ingestion, type of atom.
digestion, excretion, expulsion of  Identified by its atomic number.
excess water.  Example: Oxygens atoms no. is 8
 Nuclear Pore  Molecules
 Protein-lined channel in the nuclear  Formed when two or more atoms
envelope. joined together chemically.
 Regulates the transportation of  Examples: Oxygen, water, Nitrogen,
molecules between the nucleus and Carbon Dioxide
cytoplasm.  Compounds
 Chloroplast  Formed when two different
elements join together.
  All compounds are molecules but
not all molecules are compound.
 Examples: Water, Carbon Dioxide
ATOMS - ELEMENTS - MOLECULE - COMPOUND
 Proton
 Positive Charge of the atom
 Found in the Nucleus
 Has Charge (Positive +)
 Neutron
 No charge/ Neutral Charge
 Electron
 Located outside the nucleus.
 Has Charge (Negative -)
Definition of Terms
 Polarity
 Measure of electrical difference
within a molecule, bond, or
structure
 Non-Polar Molecule
 Molecules make of electronegatively
similar atoms, which distributes
electrons equally.
 Amphiphilic Molecule
 Some large molecules
 Organic Compound
 Almost entirely covalent bonds.
 Compounds maybe gases, liquids, or
solids
 With low melting (<360 degrees
Celsius)
 Insoluble in water, but soluble in
organic solvent such as gasoline,
benzene, carbon tetrachloride.
 Solutions in water or other solvent
do not conduct electricity.
 Almost all burn
 Reactions are usually Slow.
 Inorganic Compound
 Many compounds have ionic bonds.
 Highly melting solids (>360 degrees
Celsius)
 Many soluble in water.
 Almost entirely insoluble in organic
solvents
 Water solutions conducts electricity.
 Very few burn
 Reaction is often very fast.
 Molecules
 Tightly bound clusters of atoms.
 Holds atoms together are powerful
attractions.
 Anion
 Atoms that lose one or more
electrons
 Negatively Charge or Negative ion (-)
 Have more electron.
 Have more Negative Charge
 Examples: Br + e- → Br-
 Cation
 Positively Charge or Positive Ion (+)
 Have more protons because protons
are positively charge.
 Have more Positive Charge
*If an atom gains one or more electrons, it
becomes an ion that contains more electrons that
protons.
E.g. It has now a negative charge because it has
extra electrons. (The Bromide ion has 35 protons
and 36 electrons; the charge is -1)
 Ionic Bond
 Attraction between positive and
negative ion.
 An atom that loses one or more
electrons becomes and ION, it now
has a positive charge, Positive Ion
are called Cations.
 Examples: K- → e- + K+
 Ionic Bond
 When an electron leaves one atom
and exothermically enters into orbit
around another. There to oppositely
charged ions now attract each other.
 Generally formed between metals
and non-metals.
 E.g. Is between Na (sodium) and Cl-
(Chloride) is a silvery metal. It has 1
valence electron. Cl is a yellow-green
gas, and is needs 1 electron to fill its
 valence shell. If you put the gas and
metal together, then they will burn
as electrons are exchanged.
 The metal dissolves and the gas
disappears. The Ions now have
opposite charges and are attracted
to each other by electrostatic forces.
They from a crystal with rock salt
structure.  Electron Clouds
 Valence  Atoms are in orbitals, which are
 Outer most layer clouds of electrons.
 Capacity to attract  The orbital with the lower energy is
 Electrons called 1s Orbital
 Outer shell of atoms/ outer layer  The not orbitals, with higher energy,
 Participate in the formation of are the 2s and 2p orbitals,
chemical bond with other atom respectively.
when open  The S orbitals are spherical; all P
 Valence Shell orbitals look like dumbbells and
 Connecting the valence electrons come in sets of three.

 Octet Rule
 We use the principles that Atoms
and Ions are most stable when they
have a complete outer, shell of
electrons.
 We use this rule to predict which ion
are stable.
 Covalent Bonds
 One which atoms share a pair of
electron.
 Would a fluorine atom take an Polarity
electron from another fluorine  Polarity Molecule
atom?  A polar molecule is a chemical
o NO: Fluorine atom do not have to species in which the distribution of
take electrons from each other. They electrons between the covalently
can and do no share electron to bonded atom is not even
form a covalent bond. When they do  Non-Polar Molecule
this, both atoms have a complete  Has Even Atoms or bond is Even
octet.  Polarity
 Distribution of electrical charge over
F + F → FF the atoms joined by the bond.
F atom F atom F2 Molecule  Depende dito kung even or not
even.
 Reaction of electronegativity when
they are bonded
Example of Polar Molecule
 Water
  The most important polar molecule
on Earth
 Have a high heat capacity
 Ammonia
 Chemical Formula of Ammonia is
NH3
 (C5H5N5O).
*The existence of equal but opposite partial
charges on the atom at each end of a heteronuclear
bond (a bond between atoms of difference
elements) give rise to ab electric dipole.
Acid, Bases, And Buffers
 Acid
 Acids are substances known for their
generosity in the world of chemistry.
 Acids and bases are the most
important pharmaceutical
substances.
 Many active pharmaceutical
ingredients are insoluble in water
and aqueous solutions of such
agents cannot be prepared.
 Many acid and bases are use in the
preparation of suitable salt of drugs.
 E.g. Diclofenac sodium, atropine
sulphate
 Almost 80% of drugs are in suitable
salt form.
 Ph of acid is below 7
 Acid – Water (+)(H+)
TYPES OF ACID
o Mineral Acids
 These are derived from mineral salts
and include acids such as sulfuric
acid (H2SO4) and hydrochloric acid
(HCl).
o Organic Acids
 These are found in living organisms
and include acids such as citric acid
(C6H8O7) and lactic acid (C3H6O3).
o Amino Acids
 These are the building blocks of
proteins and include acids such as
glutamic acid (C5H9NO4) and
aspartic acid (C4H7NO4).
o Nucleic Acids
 These are the building blocks of DNA
and RNA and include acids such as
adenine (C5H5N5) and guanine
ACIDS PLAY IMPORTANT ROLES IN MANY
BIOCHEMICAL PROCESSES, INCLUDING:
o Metabolism
 Acids are involved in the breakdown
of nutrients and the production of
energy.
o Digestion
 Acids are produced in the stomach
and help to break down food.
o Protein Synthesis
 Acids are involved in the synthesis of
proteins, which are essential for
many cellular processes.
o DNA Replication
 Acids are involved in the replication
of DNA, which is necessary for cell
division and growth.
 Bases
 Bases are like the proton's best
friends.
 Bases eagerly accept protons, acting
as proton adopters in the chemical
realm.
 A base is a substance that has a pH
level above 7.4, which is the normal
pH range for most living organisms.
 Bases can also disrupt the normal
functioning of cells and tissues, and
they can be harmful to organisms.
 Hydroxide - Bases (-)(OH-)
TYPES OF BASES
o Alkaline Bases
 These are derived from mineral salts
and include bases such as sodium
hydroxide (NaOH) and potassium
hydroxide (KOH).
 o Organic Bases
 These are found in living organisms
and include bases such as ammonia
(NH3) and trimethylamine
(N(CH3)3).
o Amino Bases
 These are the building blocks of
proteins and include bases such as
histidine (C6H9NO4) and lysine
(C6H14N2O2).
o Nucleic Bases
 These are the building blocks of DNA
and RNA and include bases such as
cytosine (C4H5N3O) and uracil
(C4H4N2O2).
BASES PLAY IMPORTANT ROLES IN MANY
BIOCHEMICAL PROCESSES, INCLUDING:
o Metabolism
 Bases are involved in the breakdown
of nutrients and the production of
energy.
o Digestion
 Bases are produced in the pancreas
and help to break down food.
o Protein Synthesis
 Bases are involved in the synthesis
of proteins, which are essential for
many cellular processes.
o DNA Replication
 Bases are involved in the replication
of DNA, which is necessary for cell
division and growth.
 Buffer
 Buffers maintain equilibrium, crucial
for various biological processes.
 Picture buffers as the guardians of
pH stability, preventing chaos in the
acidity-basicity balance.
 Buffer is a substance that helps to
maintain a stable pH level in a
solution.
 Buffers work by reacting with excess
hydrogen ions (H+) or hydroxide ions
(OH-) to maintain the desired pH
level.
TYPES OF BUFFER
o Acid-Base Buffers
 These are the most common type of
buffer and consist of a mixture of a weak
acid and its conjugate base, or a weak
base and its conjugate acid.
o Protein Buffers
 These are used to maintain a stable pH
level in protein solutions and consist of a
mixture of a protein and a weak acid or
base.
o Sugar Buffers
 These are used to maintain a stable pH
level in solutions containing sugars and
consist of a mixture of a sugar and a
weak acid or base.
BUFFERS PLAY IMPORTANT ROLES IN MANY
BIOCHEMICAL PROCESSES, INCLUDING:
o Enzymes Assays
 Buffers are used to maintain a stable pH
level, which is essential for enzyme
activity.
o DNA/RNA Isolation and Purification
 Buffers are used to maintain a stable pH
level during DNA/RNA isolation and
purification, which is important for
preserving nucleic acid structure and
function.
o Protein Purification
 Buffers are used to maintain a stable pH
level during protein purification, which
is important for preserving protein
structure and function.
o Cell Culture
 Buffers are used to maintain a stable pH
level in cell culture media, which is
important for cell growth and survival.
PROPERTIES OF ACIDS AND BASES  The relative amounts of acid and base
required for complete neutralization
depend upon the total number of H+
and OH– ions produced by the
respective acid and base.

 pH Level Concentration
 the relative concentration of
hydrogen (and hydroxyl) ions in
various body fluids is measured in
concentration units called pH
 pH
 is based on the number of protons in
solution expressed in terms of moles
per liters
EXAMPLE: At a pH of 7, the scale midpoint, the
number of hydrogen ions exactly equals the
number of hydroxyl ions, therefore the solution is
Neutral

 When Acid and Bases are mixed, they

react with each other (in an exchange
reaction) and forms water and a salt

(Hydrochloric acid) (Sodium hydroxide)

HCl + NaO -> H2O + NaCl
(acid) (base) (water) (salt)

 Neutralization reaction - a type of

exchange reaction, in which an acid and
BUFFERS, ITS COMPOSITION AND
a base interact.
 In a neutralization reaction, one H+ ion MECHANISM
of acid is neutralized by one OH– ion of
the base. When all the H+ ions in the  Importance of Buffers:
acidic solution are neutralized by the  Maintaining pH Stability
same number of OH– ions of the basic  Cellular Homeostasis
solution, it is called complete  Biological Fluids
neutralization.  Enzyme Function
  Chemical Equilibria
 Composition:
 Buffers typically consist of a weak
acid and its corresponding conjugate
base or a weak base and its
conjugate acid. The most common
buffer in biological systems is the
bicarbonate ion (HCO3-) and
carbonic acid (H2CO3) system, as it
is involved in the regulation of blood
pH.
 Mechanism:
 The key to buffer action lies in the
ability of the weak acid-base pair to
donate or accept protons, thereby
preventing drastic changes in pH.
When an acid is added to the buffer
solution, the weak base component
of the buffer neutralizes the excess
H+ ions. Conversely, when a base is
added, the weak acid component
neutralizes the excess OH- ions.
EXAMPLES:
 Consider the bicarbonate buffer
system in blood. Carbonic acid
(H2CO3) acts as a weak acid, and
bicarbonate (HCO3-) serves as its
conjugate base.
 When Acid is added (e.g., HCI):
HCO3- + H+ → H2CO3
 The bicarbonate ion reacts with the
excess protons, forming carbonic
acid, preventing a significant
decrease in pH.
 When Base is added (e.g., NaOH):
H2CO3 → HCO3- + H+
 Carbonic acids dissociates to release
protons, counteracting the addition
of hydroxide ions and preventing a
substantial increase in pH.
 CHARACTERISTICS OF BUFFER SOLUTION:
 It has a definite pH.
 Its pH does not change on standing
for long periods of time.
 Its pH does not change on dilution.
 Its pH is slightly changed by the
addition of small quantity of an acid
or base.
 TYPES OF BUFFER SOLUTION:
 ACIDIC BUFFER - It is formed by the
mixture of weak acid and its salt
with a strong base.
 Example: (i) CH3COOH + CH3COONa,
(ii) HCN + NaCN, (iii) Boric acid +
Borax etc.
 BASIC BUFFER - It is formed by the
mixture of weak base and its salt
with a strong acid.
 Example: (i) NH4OH + NH4Cl (ii)
NH4OH + NH4NO3,(iii) Glycine +
Glycine Hydrochloride
 SIMPLE BUFFER - It is formed by the
mixture of acid salt and normal salt
of a polybasic acid.
 Example: Na2HPO4 + Na3PO4
 Or a salt of weak acid and a weak
base.
 Example: CH3COONH4